Interpreting the Molecular Tree of Life: What Happened in Early - - PowerPoint PPT Presentation

Interpreting the Molecular Tree of Life: What Happened in Early Evolution?

Norm Pace MCD Biology University of Colorado-Boulder nrpace@colorado.edu

Outline

• What is the “Tree of Life”?
• - Historical – Conceptually a tree of organisms, but …
• - Molecular trees, constraints, controversies and the

Next-Gen stall in expanding the Tree

• - It’s not a “simple” tree of organisms: Pangenome
• How do we know where is LUCA on the molecular map?

When was that?

• What was the nature of earliest life, the early lines of descent?
• - How to predict? How to go deeper than LUCA?
• - Paradoxes – may be interesting

Haeckel, 1866

Whittaker, 1969 Stanier, 1960s

Carl Woese, early 1980s RNase T1 fingerprint

Woese, 1977

Eukaryotes Bacteria Archaebacteria (Archaea)

Woese, 1977 1987

Eukaryotes Bacteria Archaebacteria (Archaea)

Why rRNA sequences for the backbone of the universal tree?

• Universally present
• The most conservative sequence in biology

– even into pre-cellular life.

• No lateral transfer – reflects the genetic

machinery.

Expanding the Tree: Into the Natural Microbial World

Sample  DNA  rDNA PCR library  clone  sequence “ “ “  next-gen sequence

Expansion of the Bacterial Tree

Doolittle Confusogram

Swithers and Katz, Microbe 2013

And then came genome sequences …….

Lukjancenko et al., Mic. Ecol. 6-:708 (2010) (Gene families) Tenaillon et al., Nature Rev. Microbiol. 8:207 (2010) (Genes)

Pangenome – the collection

• f genes accessible to a

“phylotype”

Strain A Strain C E.g. Gene contents of different “strains” of Escherichia coli: “Pangenome” Strain B

Strain A Strain C E.g. Gene contents of different “strains” of Escherichia coli: “Pangenome” Strain B

What’s with all the lateral transfer”?

Jed Fuhrman

5µm

Pangenome: the world of Jean-Baptist Lamark (1744-1829)

Tree of Life? Tree of what??

Tree of Life? Tree of what?? What gene(s) to use?? Core genes – rRNA, others – cellular line of descent Concatenated core genes – with care only Concatenated genomes – Ugh. There is no such thing as a tree of organisms. Note that no single gene or sequence is uniformly useful in phylogenetic analyses throughout the ToL

Making Sense of Sequences: Molecular Phylogeny

1. Align sequences so that “homologous” residues are juxtaposed.

• 2. Count the number of differences between pairs of

sequences -- this is some measure of “evolutionary distance” that separates the organisms.

• 3. Calculate the “tree”, the relatedness map, that most

accurately represents all the pairwise differences.

Experimental tree, late 1990s

Baldauf et al., 2000

Problems in resolving Deep-branching topology:

• Representation
• Uncertainty

100,000 200,000 300,000 400,000 500,000 600,000 700,000 800,000 900,000 1989 1992 1995 1998 2001 2004 2007 Cumlative Number of Sequences Total Bacteria Eucarya Archaea

5,000 10,000 15,000 20,000 25,000 30,000 1989 1992 1995 1998

A.

Now

BUT - Next-Gen Problems!!

• Next-gen sequences are short – you may get a (low level)

taxon call, but only ~70% of the time with environmental seqs and you can’t do phylogeny with “unclassified” seqs.

• Pipelines, in dealing with pyro-babble, toss novel seqs that

don’t fit the training set – and throw out the new stuff!

0. 0. 2 0. 4 0. 6 0. 8 1. 1. 2

0.0 0.3 0.5 Inferred sequence change Observed Sequence Change Unseen change Observed change

Species level variation Phylum level variation Domain level variation

* (Knuc) = -3/4 ln(1-(4/3)D) *

Woese 1987

Where is the “root” – LUCA?

• “Rooting” a tree requires an “outgroup: – not available

with a universal tree.

• Solution (Dayhoff, 1970s): “paralogous rooting” --

use trees based on in-group paralogs.

(Recall that “homologs” are of three kinds: “Orthologs”,“Paralogs” and “Xenologs.”)

Paralogs you can still recognize include:

• Elongation Factors Tu and G
• Membrane ATP Synthase α and β
• tRNAs metF and met

Each gives the 3-D tree and are homologs

EF-Tu/EF-G alignment, residues 1-70

Tu G ‐‐

Bacteria Archaea Eucarya Bacteria Archaea Eucarya

EF-G EF-Tu Rooting the Big Tree

Woese 1990

When was LUCA? >3.5 billion years ago

What was LUCA?

• Not a “genetic cell”. More likely a “state,”

communal, interdependent, replicating foci.

• Early phylogenetic lines would have differentiated

with acquisition of intermolecular specificity.

• Radiations at the base of the domains could occur
• nly after development of sophistication necessary

for independent vertical lines of descent

Paradox: How is it that chemiosmosis was

in-place before the biochemical/genetic membrane?

Maybe the first membrane was abiological.

CLASH: The Big Tree vs. the Common Wisdom

• The eukaryote nuclear line of descent is not a

late arrival, rather, is as old as cellular life

• The prokaryote-eukaryote model of evolution

is wrong and needs to be banished from the lexicon of biology.

Where did the eukaryotic cell come from?

• Mitos and chlps from specific bacterial phyla,

Proteobacteria and Cyanobacteria.

• But the nuclear line is primordial and older than

cyanobacteria

The modern kind of eucaryotic cell, complete with chloroplast (and probably mitochondrion) was in-place by >3 billion years ago !

Procaryote-Eucaryote, the textbook tale Three Domains

Models of Biological Organization and Evolution vs.

Procaryote/Eucaryote: The Test (Woese, 1977) 1. All eucaryotes are specifically related to one another. True

• 2. All procaryotes are related to the

exclusion of eucaryotes. False

• 3. Procaryotes gave rise to (more advanced)

eucaryotes. False

Organism

The End – Thank you!